#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CAF	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_deletion_substructures	i_domain	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_ref_reads_val	i_normal_vaf	i_normal_vaf_val	i_normal_var_reads	i_normal_var_reads_val	i_reference	i_refseq_mrna_id	i_rsID	i_rsID_ref_var_alleles	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_ref_reads	i_tumor_ref_reads_val	i_tumor_vaf	i_tumor_vaf_val	i_tumor_var_reads	i_tumor_var_reads_val	i_type	i_ucsc_cons	i_variant
CT47A6	728062	genome.wustl.edu	37	X	120094438	120094438	+	Silent	SNP	G	G	A			TCGA-X7-A8M8-01A-11D-A423-09	TCGA-X7-A8M8-10A-01D-A426-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	3d82a92d-1100-407d-b801-e290b1adf49a	6aeda5d6-c06b-48cf-9a2c-543e995105fd	g.chrX:120094438G>A	ENST00000443600.2	-	1	899	c.645C>T	c.(643-645)gcC>gcT	p.A215A	CT47A5_ENST00000419194.2_Intron	NM_001080141.1	NP_001073610.1	Q5JQC4	CT47A_HUMAN	cancer/testis antigen family 47, member A6	215										large_intestine(1)|lung(4)	5						TCTCCTCTGCGGCCTCCTCCG	0.687																																							0											0													13.0	34.0	30.0					X																	120094438		438	1695	2133	SO:0001819	synonymous_variant	0				CCDS35386.1	Xq24	2013-10-15			ENSG00000226023	ENSG00000226023			33287	protein-coding gene	gene with protein product	"""cancer/testis CT47 family, member 6"""	300785				16382448	Standard	NM_001080141		Approved	CT47.6	uc004eth.3	Q5JQC4	OTTHUMG00000022316	ENST00000443600.2:c.645C>T	X.37:g.120094438G>A			Q8N747	Silent	SNP	NULL	p.A215	ENST00000443600.2	37	c.645	CCDS35386.1	X																																																																																			0	NULL		0.687	CT47A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CT47A6	protein_coding	OTTHUMT00000058129.1	76	0	1.3	0.00	1	0	G	NM_001080141	0	0		120094438	-1	no_errors	ENST00000443600	ensembl	human	known	74_37	silent	91	0	9	0.00	9	0	SNP	0.054	A
TPRXL	348825	genome.wustl.edu	37	3	14105955	14105955	+	Silent	SNP	T	T	C			TCGA-X7-A8M8-01A-11D-A423-09	TCGA-X7-A8M8-10A-01D-A426-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	3d82a92d-1100-407d-b801-e290b1adf49a	6aeda5d6-c06b-48cf-9a2c-543e995105fd	g.chr3:14105955T>C	ENST00000424053.1	+	3	826	c.279T>C	c.(277-279)agT>agC	p.S93S	TPRXL_ENST00000532753.1_Intron|TPRXL_ENST00000326972.8_Silent_p.S93S|TPRXL_ENST00000429201.1_Silent_p.S93S			Q17RH7	TPRXL_HUMAN	tetra-peptide repeat homeobox-like	0	Ser-rich.									endometrium(1)	1						gcagccccagtagcagctcta	0.677																																							0											0																																										SO:0001819	synonymous_variant	0			AK092426		3p25.1	2011-06-20			ENSG00000180438	ENSG00000180438		"""Homeoboxes / PRD class"""	32178	pseudogene	pseudogene		611167					Standard	NR_002223		Approved	FLJ35107	uc003byg.3	Q17RH7	OTTHUMG00000155509	ENST00000424053.1:c.279T>C	3.37:g.14105955T>C			Q8NAM5	Silent	SNP	NULL	p.S93	ENST00000424053.1	37	c.279		3																																																																																			0	NULL		0.677	TPRXL-003	KNOWN	alternative_5_UTR|basic|appris_principal	protein_coding	TPRXL	protein_coding	OTTHUMT00000340436.1	17	5	5.26	0.00	1	0	T	NR_002223	0	0		14105955	1	no_errors	ENST00000326972	ensembl	human	known	74_37	silent	15	6	25	0.00	5	0	SNP	0.996	C
TUBBP5	643224	genome.wustl.edu	37	9	141069114	141069114	+	RNA	SNP	G	G	A	rs371804903		TCGA-X7-A8M8-01A-11D-A423-09	TCGA-X7-A8M8-10A-01D-A426-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	3d82a92d-1100-407d-b801-e290b1adf49a	6aeda5d6-c06b-48cf-9a2c-543e995105fd	g.chr9:141069114G>A	ENST00000503395.1	+	0	813									tubulin, beta pseudogene 5																		tcatcaatctgggacaggtgc	0.418																																							0											0																																												0			AF355123		9q34.3	2012-03-06	2005-11-15		ENSG00000159247	ENSG00000159247			23674	pseudogene	pseudogene			"""tubulin, beta polypeptide pseudogene 5"""			11731935	Standard	NR_027156		Approved		uc010ncq.3		OTTHUMG00000021001		9.37:g.141069114G>A				RNA	SNP	0	NULL	ENST00000503395.1	37	NULL		9																																																																																			0	0		0.418	TUBBP5-003	KNOWN	basic	processed_transcript	TUBBP5	pseudogene	OTTHUMT00000373087.1	39	7	2.44	0.00	1	0	G	NR_027156	rs371804903	G->A		141069114	1	no_errors	ENST00000503395	ensembl	human	known	74_37	rna	51	10	8.93	0.00	5	0	SNP	0.015	A
LTK	4058	genome.wustl.edu	37	15	41803413	41803413	+	Missense_Mutation	SNP	C	C	G			TCGA-X7-A8M8-01A-11D-A423-09	TCGA-X7-A8M8-10A-01D-A426-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	3d82a92d-1100-407d-b801-e290b1adf49a	6aeda5d6-c06b-48cf-9a2c-543e995105fd	g.chr15:41803413C>G	ENST00000263800.6	-	7	1042	c.946G>C	c.(946-948)Ggg>Cgg	p.G316R	LTK_ENST00000355166.5_Intron|LTK_ENST00000561619.1_Intron|LTK_ENST00000453182.2_Intron	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	316					cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		ccgccgcccccgaagccgccg	0.781										TSP Lung(18;0.14)																													0											0													2.0	3.0	2.0					15																	41803413		804	1920	2724	SO:0001583	missense	0			D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"""leukocyte tyrosine kinase"""			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.946G>C	15.37:g.41803413C>G	ENSP00000263800:p.Gly316Arg		A6NNJ8|B4DL89|E9PFX4	Missense_Mutation	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.G316R	ENST00000263800.6	37	c.946	CCDS10077.1	15	.	.	.	.	.	.	.	.	.	.	C	15.04	2.714588	0.48622	.	.	ENSG00000062524	ENST00000360087;ENST00000263800	D	0.86230	-2.09	3.93	3.0	0.34707	.	.	.	.	.	D	0.89128	0.6627	M	0.79123	2.44	0.80722	D	1	P	0.43314	0.803	P	0.51945	0.685	D	0.87498	0.2431	9	0.87932	D	0	.	5.0433	0.14471	0.2037:0.687:0.0:0.1093	.	316	P29376	LTK_HUMAN	R	316	ENSP00000263800:G316R	ENSP00000263800:G316R	G	-	1	0	LTK	39590705	0.861000	0.29849	0.411000	0.26484	0.966000	0.64601	1.595000	0.36708	0.865000	0.35603	0.644000	0.83932	GGG	0	NULL		0.781	LTK-001	KNOWN	basic|CCDS	protein_coding	LTK	protein_coding	OTTHUMT00000252690.2	22	18	0	0.00	0	0	C		0	0		41803413	-1	no_errors	ENST00000263800	ensembl	human	known	74_37	missense	14	10	22.22	0.00	4	0	SNP	0.958	G
PLET1	349633	genome.wustl.edu	37	11	112118603	112118604	+	IGR	DEL	TA	TA	-			TCGA-X7-A8M8-01A-11D-A423-09	TCGA-X7-A8M8-10A-01D-A426-09	TA	TA					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	3d82a92d-1100-407d-b801-e290b1adf49a	6aeda5d6-c06b-48cf-9a2c-543e995105fd	g.chr11:112118603_112118604delTA	ENST00000338832.2	-	0	1541				AP002884.1_ENST00000401135.1_RNA	NM_001145024.1	NP_001138496.1	Q6UQ28	PLET1_HUMAN							cell differentiation (GO:0030154)|negative regulation of cell-matrix adhesion (GO:0001953)|positive regulation of cell migration (GO:0030335)|wound healing, spreading of epidermal cells (GO:0035313)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)				endometrium(2)	2						tatatatatgtatatATacaca	0.356																																							0											0																																										SO:0001628	intergenic_variant	0																															11.37:g.112118609_112118610delTA			Q6UQ24|Q6UQ25|Q6UQ27	RNA	DEL	0	NULL	ENST00000338832.2	37	NULL		11																																																																																			0	0		0.356	C11orf34-201	KNOWN	basic|appris_principal	protein_coding	ENSG00000215954	protein_coding		50	0	0	0.00	0	0	TA		0	0		112118604	1	no_errors	ENST00000401135	ensembl	human	novel	74_37	rna	37	0	7.5	0.00	3	0	DEL	0.045:0.054	0
